bild
School of
Computer Science
and Communication
Me

Jens Lagergren

<jensl@nada.kth.se>
Telephone: +46 8 55 37 85 70, fax: +46 8 55 37 82 14
Address: KTH, Albanova, SBC, S - 100 44 Stockholm
Visiting address: Albanova, Roslagstullsbacken 35 (see directions and map)
(Denna sida finns ej tillgänglig på svenska.)

Affiliation

I am professor in computer science and computational biology in CB (the Computational Biology department) of CSC. I also belong to SBC (Stockholm Bioinformatics Center). SBC is a joint venture between KTH (Kunliga Tekniska Högskolan, i.e., The Royal Institute of Technology) and SU (Stockholm University). SBC was initially funded by the Swedish Foundation for Strategic Research. Fortunately, CB and SBC are are currently located in the same building. For directions see directions and map to SBC..

Current Courses

Research Group

Ph.D. Students

Former Post-docs

Former Ph.D. Students

Recent Service

Co-chair program committee WABI 2008
Program committee RECOMB 2008
Program committee ISMB 2007
Program committee WABI 2007.
Program committee RECOMB 2007
Program committee ISMB 2006
Program committee WABI 2006.
Chair program committee Bioinformatics 2006.
Co-organizer Bertinoro Computational Biology Workshop 2006
Program committee CompBioNets 2005
Program committee 3rd RECOMB Satellite Workshop on Comparative Genomics, 2005
Program committee WABI 2005.
Program committee ISMB 2005
Member of the BICI Scientific Advisory Board
Chair program committee Second RECOMB Satellite Workshop on Comparative Genomics, 2004.
Co-organizer Second RECOMB Satellite Workshop on Comparative Genomics, 2004.
Program committee Bioinformatics 2005.
Program committee WABI 2004
Program committee RECOMB 2004
Board member of SocBiN -- Society for Bioinformatics in the Nordic countries.

Refereed Publications since 2000 (in most cases authors are listed in alphabetic order, i.e. computer science style)

Motif Yggdrasil: Sampling from a Tree Mixture Model.
Samuel A. Andersson and Jens Lagergren.
In Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB 2006), pages 458-472.
Genome-wide survey for biologically functional pseudogenes.
Ö.P. Svensson, L. Arvestad, J. Lagergren
PLoS Computational Biology Vol. 2, No. 5, e46 DOI: 10.1371/journal.pcbi.0020046
New Probabilistic Network Models and Algorithms for Oncogenesis.
M. Hjelm, M. Höglund, and J. Lagergren.
Journal of Computational Biology, May 2006, Vol. 13, No. 4: 853-865.
Compatibility of unrooted phylogenetic trees is FPT.
D. Bryant and J. Lagergren.
Theoretical Computer Science 351 (2006) 296-302
Fast Neighbor Joining.
I. Elias and J. Lagergren.
ICALP 2005, pages 1263--1274
Algorithms for RH Mapping: New Ideas and Improved Analysis.
L. Ivansson and J. Lagergren.
SIAM Journal on Computing 34(1):89--108 (2005)
MSCAN: identification of functional clusters of transcription factor binding sites.
W. Alkema, Öjvind Johansson, Jens Lagergren, and Wyeth W. Wasserman
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W195-8.
PDF
Ancestral Maximum Likelihood of Phylogenetic Trees is Hard
L. Addario-Berry, B. Chor, M. Hallett, J. Lagergren, A. Panconesi, and T. Wareham.
Journal of Bioinformatics and Computational Biology, January 2004, 12:55
doi:10.1142/S0219720004000557
Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution
Lars Arvestad, Ann-Charlotte Berglund, Jens Lagergren, and Bengt Sennblad
RECOMB 2004, 326-335.
PS
Simultaneous Identification of Duplications and Lateral Transfers
M. Hallett, J. Lagergren, and A. Tofigh
RECOMB 2004, 347-356.
PDF, PS
Ancestral Maximum Likelihood of Phylogenetic Trees is Hard
Louigi Addario-Berry, Benny Chor, Mike Hallett, Jens Lagergren, Alessandro Panconesi, and Todd Wareham
WABI 2003: 202-215
PS A4, PS Letter
Fitting Point on the Real Line and its Application to RH Mapping
J. Håstad, L. Ivansson, and J. Lagergren
J. Algorithms 49(1): 42-62 (2003)
PDF
A polynomial-time algorithm for near-perfect phylogeny
D. Fernandez-Baca, J. Lagergren
SIAM Journal on Computing 32(5): 1115-1127 (2003)
PDF
Bayesian Gene/Species Tree Reconciliation and Orthology Analysis Using MCMC
L. Arvestad, A.C. Berglund, J. Lagergren, and B. Sennblad
Bioinformatics (ISMB) 2003: 7-15
PDF
Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm
Öjvind Johansson, W. Alkema, Wyeth W. Wasserman, and Jens Lagergren
Bioinformatics (ISMB) 2003: 169-176
PS PDF
Towards Identifying Lateral Gene Transfer Events
L. Addario-Berry, M. Hallett, J. Lagergren
Pacific Symposium on Biocomputing 2003: 279-290
PDF
Combining Polynomial Running Time and Fast Convergence for the Disk-Covering Method
J. Lagergren.
Journal of Computer and System Science, 65(3): 481-493 (2002)
Efficient Algorithms for Lateral Gene Transfer Problems.
M.T. Hallett and J. Lagergren.
In RECOMB´01, pages 149-156.
Hunting for Functionally Analogous Genes.
M.T. Hallett and J.Lagergren.
In FSTTCS´00.
New algorithms for the duplication-loss model.
M.T. Hallett and J.Lagergren.
In RECOMB´00, pages 138-146.
PDF

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Published by: <jensl@nada.kth.se>
Updated 2009-06-11

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